Brokers often offer 2 types of accounts: Netting (FIFO) and Hedging. The Trade Copier supports the 2 types. The Trade Copier will copy the trades according to the account type. For instance, if you do not want Netting (FIFO), simply use a Hedging account for your Slave and/or Master.
It's at your broker side. You have to reach out to your broker to change the settings.